Closed aksarkar closed 5 years ago
Minimal example:
> train = readRDS("train.Rds") > c = ashr:::ash.estmode(rep(0, nrow(train)), sebetahat=1, modemin=0, modemax=2, lik=ashr::lik_pois(y=train$x, scale=train$scale, link="identity")) Error in is.list(x) : invalid 'times' argument > traceback() 13: stop(e) 12: value[[3L]](cond) 11: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) { e$call <- cl.i stop(e) }) 8: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) { e$call <- cl.i stop(e) }), warning = function(w) { w$call <- cl.i w }) 7: stopifnot(is.list(x), is.list(val)) 6: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df, ...), list(call = match.call())) 5: ash(betahat = betahat, mode = c, outputlevel = "loglik", ...) 4: f(arg, ...) 3: (function (arg) f(arg, ...))(1.23606797749979) 2: stats::optimize(test.op, interval = c(modemin, modemax)) 1: ashr:::ash.estmode(rep(0, nrow(train)), sebetahat = 1, modemin = 0, modemax = 2, lik = ashr::lik_pois(y = train$x, scale = train$scale, link = "identity")) > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Scientific Linux 7.4 (Nitrogen) Matrix products: default BLAS/LAPACK: /scratch/midway2/aksarkar/miniconda3/envs/scmodes/lib/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] MASS_7.3-50 compiler_3.5.1 Matrix_1.2-14 parallel_3.5.1 [5] mixsqp_0.1-97 Rcpp_0.12.18 codetools_0.2-15 SQUAREM_2017.10-1 [9] pscl_1.5.2 doParallel_1.0.11 grid_3.5.1 iterators_1.0.10 [13] foreach_1.4.4 truncnorm_1.0-8 ashr_2.2-32 lattice_0.20-35
Data is available here https://users.rcc.uchicago.edu/~aksarkar/singlecell-ideas/train.Rds
Sorry closed by accident. please Close if it works!
646154b did fix it.
It might be helpful to add a test case with this example dataset to make sure nothing else breaks in tricky places.
Minimal example:
Data is available here https://users.rcc.uchicago.edu/~aksarkar/singlecell-ideas/train.Rds